


Merlin in the matrix

by Cookietree



Category: Merlin (TV), The Matrix (Movies)
Genre: M/M
Language: English
Status: In-Progress
Published: 2020-04-15
Updated: 2020-04-20
Packaged: 2021-03-02 04:28:07
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence, Major Character Death
Chapters: 2
Words: 3,251
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/23669152
Author URL: https://archiveofourown.org/users/Cookietree/pseuds/Cookietree
Summary: An AU where Merlin is prophesied by the oracle, Killgarrah,  to be "the one,". "The one," being the most powerful person in the Matrix who can help the once and future King come back to Albion when the need is greatest. Albion is currently a barren, desolate wasteland under the heart of the AI's control. Repeatedly in his dreams, Merlin is led by a handsome stranger into an underground world where he meets Gauis. A rumored individual who is thought to be one of the most knowledgeable and can answer some of Merlin's questions. Such as, what is the matrix?A merlin and matrix crossover with slow-burn merthur oho!
Relationships: Merlin & Arthur Pendragon (Merlin), Merlin/Arthur Pendragon (Merlin)
Comments: 11
Kudos: 7





	1. Chapter 1

**CHAPTER 1 - PROLOGUE**

"Is everything in place?" a low voice spoke, sounding crackly with the interference.

"I thought you didn't believe me?" a woman replied in a slightly amused tone.

"I know, but I felt duty-bound to help Gauis,"

"Don't lie to your sister, you like him, don't you? You like watching him,"

"Ha! Don't be ridiculous, he's a complete idiot"

"Yes and he's probably going to end up getting killed,"

"For some reason Gauis believes he's the one,"

"Do you believe he's the one?"

"No of course not,"

"Then, do you think Gauis is a liar?"

"No, I'm calling you a fool," 

Suddenly, there was a faint guttural sound in the background which sounded oddly mechanical. 

"Did you hear that?" he whispered.

"Hear what?"

"Are you sure this line is clean?"

"Yeah of course I'm sure"

"..."

"..."

"I think... I better go,"

"Good luck, "

* * * *

Several beams of light were scouring the dark, dank hallways inside of what looked like a run down hotel. The leading figure of the group (of around 10 individuals) made sure to usher the other fire-armed operatives in his direction. 

He motioned and pointed his torch at the door of a room numbered 303.

"FREEZE POLICE!" he screamed, kicking down the door violently, "PUT YOUR HANDS IN THE AIR! NOW!" the other operatives followed him in, quickly filling up the small dingy room.

All torches, guns and eyes were fixated on one single man facing the wall in front of them. He was dressed completely in black with skinny trousers and a shiny leather jacket. The man didn't react or even say anything but raised his hands up slowly and submissively.

One of the operatives put a hand to his earpiece, "They're sending the witchfinders up,"he told their captain.

"What?" The captain gawked in surprise, "Can't they trust us to deal with a single guy?" 

"Apparently not,"

Taking advantage of their slight distraction, the single man noticed one of the men getting too close to him, appearingly trying to handcuff him. Like a praying mantis, he grabbed his arm then flipped him over before sending a quick knockout blow to the head.

The other guys rushed towards him, yelling.

In response, he kicked a chair at a few of them, sending them into a wall. You could hear many groans of pain, he'd easily broken many of their bones. The rest of them panicked and let bullets loose on the man as a last resort, but like a warrior monk, he somehow ran up the side of the wall dodging them easily with inhumane speed. Then he grabbed another operative, using them as a human shield, snatching their gun to mow the remaining operatives down. 

"I'm in deep shit," He muttered. Quickly dialing a number, he placed a flip phone to his ear, "Gauis, somehow they traced the line, the witchfinders are coming for me,"

"I know,"

"What do I do!?"

"There's little time before they come, you _need_ to find another exit,"

"Where's the nearest one?"

"In the next apartment,"

"Right,"

"I know you can make it Arthur," The voice replied, "Now go!"

Arthur hung up abruptly, stuffing the phone into his pocket before sprinting out of the room into the hallway, he could hear the footsteps of the witchfinders quickly closing in behind him. He flew around a corner, narrowly missing bullets, before reaching a metal stairway then climbed up six flights that reached the flat rooftop of the hotel.

Without stopping for breath, he legged it, dodging left and right, using the chimneys as shields against the further gunshots chasing him. Then, without a moment of hesitation, he leaped across the width of a street before diving into the window of a random apartment headfirst. 

Laying on the ground dazed for a second, a granny in her sitting room screeched at him. He couldn't waste anymore time. He forced himself to move towards her telephone, he could hear it ringing. Arthur snatched the phone, panicking as he picked it up noticing the granny had already morphed into a witchfinder. 

Arthur recognised that face bitterly. 

As Agent Uther pulled the trigger, Arthur vanished just in time, letting the bullet embed itself in the wall behind where he previously stood. 

Uther stood silently for a little while, before the other witchfinders gathered up behind him. One of them came up to him, 

"You let him get away," they drawled, listlessly.

"It doesn't matter if the informant is real," Uther replied, his voice cold and smooth like ice. 

"Yes,"

"We have the name of their next target?"

"Yes my lord, the name is Merlin,"

"We need to search for him,"

"The search has already begun,"

"Goood,"


	2. Merlin

**Summary for the Chapter:**

> Merlin gets into some shit and meets a handsome stranger... I wonder who on earth that could be? *Grins wickedly*

A dark haired, scrawny figure lay asleep hunched over his computer desk. His room was small, untidy and dingy with lots of scattered computer screens surrounding him, their artificial light being the only thing illuminating the darkness. The boy stirred a little, blearily opening his eyes a fraction to witness his computer typing him a message.

" **Wake up Merlin...** " it said.

Blinking in surprise, he sat up abruptly. His mind reeling as he could not remember having programmed his computer to wake him up in the mornings. _Actually wait, was it morning?_ He stared at the screen before witnessing the message deleting itself, before another one appeared:

" **The matrix has you.** "

He took a sharp intake of air, _now that sounded undoubtedly ominous_. The message then deleted and replaced itself again:

" **Follow the white dragon.** "

"The what now!?" Merlin said aloud, gawking stupidly. He looked around as if expecting a dragon to suddenly appear in his room.

" **Knock, knock, Merlin**."

Immediately, two knocks sounded on his door, making Merlin jump out of his skin. Perhaps trembling a little, he stepped towards it and opened it cautiously.

"Merlin!" A familiar voice exclaimed.

"Will," Merlin breathed in relief.

The guy grinned at Merlin, a girl standing behind him, "Fancy coming along to the tavern with us?" he asked, "This is my new friend Aithusa," he gestured at her.

"I... I'm not sure if I can," Merlin began, he needed to stay at home, figure out what those messages was all about.

"That's too bad, are you sure you can't come with us?" The girl hugged Will across his shoulders, leaning her head backwards, exposing her neck. "It'll be fun,"

Merlin almost choked, spying a white dragon tattoo there, he stared at it in shock for a few seconds.

"Um, alright sure,"  
  
  


* * * *  
  
  


Inside the tavern, the air was heavy with sweat and alcohol and the strobe lighting on the dance floor was intensely disorientating. Merlin stood alone leaning on a wall having lost Will and his new female friend amongst the sea of people moving to loud Grunge music.

Merlin suddenly felt something strange, someone was staring at him. He shivered, before turning around cautiously, meeting eye to eye with a blonde man.

"Hello Merlin," the stranger said, in a mocking tone.

Merlin's jaw dropped a little at the guy, shocked by a beautiful face. It was well defined and had strong angular eyebrows that a nobleman would have. And his eyes, those intense blue eyes were glaring directly at him.

"How do you know my name?" he managed to choke out.

"I know a great many things about you, such as how much of a wimp you are, for starters," he stepped forward.

"Sorry what?" he felt himself grow a bit irritated.

The stranger only sighed in exasperated response, before he glared at Merlin again looking him up and down as he spoke stiffly "I can't believe that _he_ thinks _you're_ the one,"

"Look," Merlin glared back at him, "I don't know how I've offended you, but, can you go speak gibberish at someone else please?"

"Unfortunately I can't, because _he_ sent me to talk to you,"

"What do you mean by he?" Merlin demanded, "Who's this he you keep going on about?"

"You know _who_ I mean and you know I'm _not_ speaking gibberish Merlin," The stranger pressed his body close to Merlin's, his mouth was very close to his ear, so very close, Merlin could feel his hot breath on his neck, "now focus on this message so it gets through that thick skull of yours - I'm here to warn you about something,"

Merlin's eyes widened in shock, he felt distinctly uncomfortable by their sudden close proximity and intimidated by how sombre this conversation was becoming.

"Right now, all I can tell you is that you are in danger, and that they're watching you Merlin,"

"Who?"

"You need to listen to me, normally if they found out who our target was, we'd leave you alone and keep you out of danger, but, you're different because of _his_ belief in you being 'the one,'."

"Right..." Merlin replied, unsure of what to believe.

"You came here because you wanted an answer, an answer to every hacker's question,"

"I don't know about that,"

"Ah, but you do know, even an idiot like you knows what the question is,"

Merlin thought for a moment, before it came apparent to him,

"What is the matrix?" he breathed, feeling instantly like he shouldn't have said that question aloud.

The man leaned back and gave a small nod at him, "Twelve years ago, I met _him_ and _he_ told me that nobody could be told the answer to that question,"

"What's the point of all this then?"

"Let me finish, God, you really are as much as a fool as you look, " He sighed, "you have to be shown the answer - otherwise you won't believe it. When he finds you, you have to let him show you the answer. But to be shown the answer, you have to choose, be willing to let everything change but you're such a coward I'd doubt you would choose to find out,"

"You don't know that," Merlin said wryly.

"That's all I can tell you, I need to leave, I'm running out of time,"

"Wait! Who the hell are you?" Merlin yelled angrily. 

"Who me?" He laughed, "Arthur,"

"What?" he scoffed, "The Arthur?" Merlin couldn't believe this. The legendary hacker? The guy who cracked the I.R.S Kansas City D-base!?

"Yeah," the man smirked, " _the_ Arthur,"

"You know," Merlin taunted, "I had imagined you somewhat differently,"

"Oh?"

"Yeah, as much less of an arrogant ass,"

Arthur only sighed again, "And I you, less of an idiot. Goodbye Merlin,"

Abruptly, the music began to feel too loud, it started clanging around in his head. Merlin felt strange, he blinked once and Arthur had disappeared. He blinked again, and a repeating note was the only thing he could pick out from the music.

The sound swelled larger and larger, until he realised that it was the sound of an alarm clock.

His consciousness was being forcibly dragged out of him, he reluctantly opened his eyes seeing that he was in a different room and that the time was 9:05 am.

"Oh no!" he wailed, "I'm going to be late!" his boss was not going to be pleased. But then again, when was his boss ever pleased?  
  
  


* * * *  
  
  


"How many times now has it been? Hmm? Tell me Merlin" a balding middle aged man muttered, looking at his computer screen, he was the head of the software company Merlin worked for.

"Uh," Merlin's attention was seemingly elsewhere, looking outside.

"How many times now have you come late to work?" The man raised his voice, now staring directly at Merlin.

"Well I," Merlin came back to reality, fumbling on words a bit.

"You don't know? Neither do I, because I've lost count,"

"I'm very sorry Mr Curran,"

"So am I Merlin," he responded bitterly, "Honestly if you turn up late again, you'll have to find yourself another job, am I making myself clear to you?"

"Yes Mr Curran," Merlin replied, trying to sound serious.

Mr Curran sneered, obviously not impressed by Merlin's lack of work ethic, "You obviously think that you're so special, that rules do not apply to you,"

"No, I don't" he replied quickly.

"Then why are you blatantly coming to work late so often? You clearly have a problem, "

"Mr Curran I..." 

"I don't have time for this, go back to your desk," he sharply interjected.

"Yes Mr Curran," Merlin frowned.

****

Merlin left the office, striding into his own workplace, before a voice interrupted, coming from the door of his cubicle.

"Mr Hunithson?"

Merlin jumped a bit, before he glanced at some lanky delivery man who was holding out a package.

"That's me." he replied.

"Here," the man said, before he handed it to him.

"Thank you," Merlin smiled. He then signed the electronic pad offered to him, before taking it to his work cubicle in the office, and teared the package open.

Inside the package was a flip phone, and much to his astonishment, it was ringing.

Merlin's eyes widened. This was a strange package indeed and normally he wouldn't trust such a thing. Yet, for some reason, his instincts were screaming at him to pick up the phone and put it to his ear. He mulled it over for a second, before deliberating that he had nothing to lose from listening to a single phone call - it wasn't like anyone could leap out of the phone and attack him or suck him away to another world, he laughed at himself.

Gripping the phone tightly to his ear, he mustered courage and asked, "Hello?"

"Hello Merlin, my name is Gauis," the sound of a dodgery old man replied.

Merlin's knees knocked together a little bit as he tried not to sink into his chair in shock.

Could this be _him_? Was this the guy Arthur wouldn't stop going on about? Something inside Merlin was telling him that this was him.

"I had hoped to speak to you during less treacherous conditions, but it seems I could not count on hope today," Gauis went on.

"Right," Merlin's heart thumped against his chest at the mention of treacherous conditions.

"I do not know if you're ready to be in a position to choose today Merlin, but, it looks like we have little time left. You must know that you are special and we can't allow any harm to come to you. You must also know that they're coming for you. I'm not sure what they're going to do when they find you, but it can't be anything good,"

"Who are _they_?"

"Stand up boy, and see for yourself,"

"Now?"

"Yes Merlin, now," he paused a second before he said, "stand up slowly and look towards the elevator,"

Trembling a little, he did as Gauis instructed before immediately sitting back down again.

He had just seen a group of menacing armed men, suited in black, stepping calmly out of the elevator, an elevator, just like Gauis had said. This was like when the computer was predicting what was going to happen yesterday. How was this all happening? Merlin thought wildly, this must all be linked in some way.

Oh dear God, that meant that Gauis was also right about predicting the oncoming 'treacherous conditions'. He started to panic.

"Gauis, what do they want with me?" He muttered quietly, so _they_ couldn't hear him.

"I'm not sure, but if you don't want to find out, I think you better get yourself out of there,"

"How do I do that!?"

"I can guide you Merlin, but you must do exactly as I say," he urged.

Merlin could hear their footsteps getting closer to his work cubicle, "But.. I"

"Go!" 

Without thinking, Merlin felt himself lunging across the hall to the cubicle opposite him, just as the suited men turned into his row.

Merlin crammed himself into a dark corner, underneath a desk, silently praying that _they,_ whoever _they_ were, wouldn't find him. 

"Stay there for a moment," the voice reassured.

One of the suited men entered Merlin's empty cubicle. He looked up and motioned at an officer that had accompanied them to go search in the bathroom. Up ahead, Mr Curran stood speaking to another suited man and an employee.

"Now wait a little longer...When I tell you to, you must go to the end of the row to the first office on your left and stay as low as you can" 

A drop of sweat trickled down Merlin's forehead as Merlin held onto his breath, staying deathly silent as the man left his cubicle and went to join Mr Curran.

"Now,"  
  


Merlin rolled out of the cubicle, his eyes popping as he froze behind another suited man that had just turned around in that moment facing away from him. Staying crouched, he sneaked down the row, shooting across the opening to the first office on his left.

The room was empty. 

Thank God.

"Good, well done Merlin. Now, there is a window in front of you. Open it."

"How do you know all of this?" Merlin couldn't help himself asking.

"All in good time, my dear boy," Gauis merely laughed.

Merlin opened the window steadily, flinching as the wind whooshed and howled around the room, he looked upon the streets far below him and at the much too narrow ledgeways on the front of the building. How on earth was he going to escape?

"Now, do you see a scaffold outside? You can use that to get to the rooftop,"

Merlin spied it several offices away.

"That's too far away! It's too dangerous!" Merlin exclaimed.

"There's a small ledge and it's a short climb. You can most certainly make it, boy,"

Merlin looked down again, the building's walls sunk into the concrete chasm below. His head reeling, he was breathless from the vertigo.

"No," he whispered, "No way, this is madness Gauis,"

"You can't allow yourself to be controlled by fear Merlin,"

"There must be some other way,"

"I'm afraid there isn't, there are only two ways out of the building you are in. One way is at that scaffold or the other is in their custody. I must go, it's up to you now."

There was a clicking sound as Gauis hung up. Merlin was left to make his decisions alone and he didn't know what to do. He repeatedly glanced between the door and the scaffold, desperately racking his brain as to whether it would be worth risking his life to avoid whoever these dodgy guys were.

"This is insane! I am just a nobody and I always will be, in no way shape or form am I in anyway special! Why on Earth is this happening to me? I didn't do anything!" he muttered darkly to himself.

Damn it all, Merlin gritted his teeth and climbed onto the window ledge. Clinging onto the frame for dear life, he cautiously stepped onto the narrow ridge below.

Peering at the scaffold again, somehow it seemed even further away than it had been before.

"This is going to kill me, if I fall, that's it, I'm dead," he uttered to himself. The wind seemed to agree with him as it blasted up the front of the building, knocking Merlin off balance. Recoiling, he clinged even closer to the frame, his trembling hands dropped the phone.

He watched it fall. 

He held his breath as he watched it being swallowed by the sheer distance beneath him.

"I can't do this," Merlin swallowed, "I just can't,"

Fear overtook him as he climbed back into the office just as he heard the office door opening. 

"FREEZE!" 

**Notes for the Chapter:**

> Hello all, this is my first fanfic on archiveof as well as my first merthur fanfiction. I hope you enjoy! I also hope I can combine these two worlds effectively and that this story doesn't end up being a complete shambles. Please leave a comment to let me know what you think! Thank you! :)


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